//
// Strelka - Small Variant Caller
// Copyright (c) 2009-2018 Illumina, Inc.
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program.  If not, see <http://www.gnu.org/licenses/>.
//
//

///
/// \author Chris Saunders
///

#pragma once

#include "gvcfAlleleInfo.hh"
#include "blt_util/reference_contig_segment.hh"


/// create information required for reporting a multi-ALT locus in VCF format
///
void
getLocusReportInfoFromAlleles(
    const reference_contig_segment& ref,
    const std::vector<GermlineIndelAlleleInfo>& indelAlleles,
    unsigned commonPrefixLength,
    OrthogonalAlleleSetLocusReportInfo& locusReportInfo);
